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Eventually, we should come up with some nice format for articles about chemical compounds. Right now, I like caffeine: a picture of the 3-d structure, a picture of the chemical structure, the chemical formula and the correct name. Maybe the CAS number should be added for completeness. I know that 3-d structure images can be produced with the program rasmol. Does anyone know a nice program for producing the 2-d structure formulas? Right now, I use JChemPaint and I don't like it. AxelBoldt 03:36 Dec 17, 2002 (UTC)
I've used molpov before. its pretty cool. it takes a .mol file and creates 2d or 3d POV renderings out of them. its really powerful and slick. but you do needa POV program for it to work (I use PovRay) both of those are freeely available. either frreeware or maybe even Free Software, I don't remember at the moment. Lightning 22:41, 13 Aug 2003 (UTC)
The 3D picture on caffeine is way too dark -- I can't see much at all on my monitor. A lighter background would be better -- grey, or the same shade of cream as the 2D diagram. -- Tarquin (but apart fomr that, caffeine is good. I've been editing articles on compounds to open with:
Discussion of the table for inorganic compounds given at Inorganic table information should probably take place here... AxelBoldt 23:04 22 May 2003 (UTC)
Has any consensus been reached on how to name articles describing chemical compounds. Obviously, there are cases where the systematic name for the compound is not the appropriate name for the article. An extreme example would be water. And since the sort of chemicals that are of sufficient industrial, historical, or pharmacological importance to merit articles are exactly the sort of compounds likely to be better-known known by a common name than their systematic one, I guess, how should we decide? Take the Google poll? Use whatever comes first in a standard reference like the Merck index? Any other thoughts?
Shimmin 04:14, 22 Aug 2003 (UTC)
Have it both ways. Redirect
Usually I would have the trivial name as the primary page, since that's what most people will be searching on if they don't know much about it - unless the trivial name is actually obsolescent. Have a redirect from the IUPAC name if it's reasonably compact and likely to be easy to type without errors. For the really hard IUPAC names, they might just have to rely on the search function - which implies all chem pages should include the IUPAC name in the text. -- Roger 10:08, 03 Sep 2003 (UTC)
Chemical Structure Program
Can anyone recommend a decent free program that draws chemical structures. One that's not too hard and runs under Windows or Linux would be great. ThereIsNoSteve 05:29, 29 Sep 2003 (UTC)
One program is xymtex, that someone has used to do the steroid hormones. e.g. Image:Testosterone.png. I've never used it, so i can't tell you anything about it. I guess it's similar to Latex etc. (haven't used that either) Tristanb 06:04, 29 Sep 2003 (UTC)
I searched around for a while and the best I could come up with was ChemSketch; it's freeware for Windows, but not open source. In the long run, we need (and will certainly get) something like our wikipedia:TeX markup feature which would allow you to specify a molecule structure in TeX and it's typeset automatically. AxelBoldt 16:47, 29 Sep 2003 (UTC)
I agree about the TeX. There a whole lot of (La)Tex packages out there that support typesetting technical things like chemical structures, syntax trees, mathematical plots, Feynman diagrams, phonetic symbols, Karnaugh maps, etc, that would otherwise have to just be made by hand and uploaded as an images. The downside of this is that there is nothing ensuring consistency in style of the diagrams, and modifying the bitmaps is non-ideal. Being able to edit the TeX source, while not extraordinarily easy, would be more in keeping with wiki style. Plus, if we get really clever, we could generate higher-resolution versions for print pages. Before I got sucked in to the whole logo-debate and modifications, I was working in the background on modifying the TeX support in MediaWiki to support phonetic symbols, but it seems abstracting it to support a variety of packages would be the best solution. On the other hand, SVG images for a lot of this stuff would probably be better. -- Nohat 18:05, 29 Sep 2003 (UTC)
Personally, I use ChemSketch (I forget the site). You can make images out of the chemical structures simply by copy pasting from ChemSketch to your favorite image program (such as IrfanView or Paint). Certain things don't work, though (including phosphate groups, I couldn't make the structure for ATP because of that). ugen64 20:04, Nov 22, 2003 (UTC)
ISIS Draw is not open source or any such, but is not bad for a windows box. Personally, I use the entirely-not-free CS Chemdraw - it is the best by some way. Iridium77 17:44, 23 Feb 2004 (UTC)
If consistency of style is important, the ideal solution would be to have the wiki-code be a SMILES string, from which an onsite application would generate a chemical structure. ChemDraw does this, and there is at least one applet on the web that does it. I have no idea what would be involved in coding up such a function for the wiki, though. Shimmin
That's okay for simple stuff, but for anything more complicated, it becomes irritating to not be able to define the orientation that you actually want in the diagram. For some things, it's impossible: try getting any app to draw a metallocene legibly from SMILES :-)
I've done many structures with PPCHTeX, like nicotine, omeprazole and fluphenazine. I don't know what you think about it; when it works, it works, but I suspect there are more flexible methods that work in all cases. [[User:Sverdrup|User:Sverdrup]] 23:20, 15 Aug 2004 (UTC)
The lack of a symbol for equilibrium
Unless anyone objects, the standard wikipedia symbol for equilibrium will be ↔, until someone fixes this problem. Resonance will need another symbol.
Other options that shouldn't be used for equilibrium are:
<->
<=>
Software
The current wikipedia software simply doesn't work for chemistry. Until better software is created, chemistry will not be worth adding to wikipedia. Bensaccount 20:38, 6 Mar 2004 (UTC)
I hope you're being sarcastic. For years, chemical knowledge has been distributed using an outdated technology that has no chemistry-specific functions, and science carried on fine. We should decide on what a good chemical diagram should look like, but I don't think there are any issues with putting chemistry on here.
Yes, I have changed my mind. A lot of chemistry can be explained using IUPAC nomenclature. Bensaccount 18:05, 9 Mar 2004 (UTC)
IUPAC nomenclature doesn't explain anything, it is a set of rules as to how you name things. Many common chemicals are known more often by their common names rather than IUPAC. Diagrams are fine the way they are, but would be better if we standardised them. Iridium77 22:02, 9 Mar 2004 (UTC)
IUPAC nomenclature allows you to explain the structure of a compound without a diagram. Common nomenclature is outdated. Bensaccount 03:49, 6 Apr 2004 (UTC)
Which is fine, if you are a computer, and no errors were made in communicating the systematic name. The persistance of common names for many of the most industrially important compounds, however, indicates that for all but the most trivial cases, we as humans are better at memorizing non-systematic names than interpreting systematic ones. Shimmin 04:18, 6 Apr 2004 (UTC)
Ben, to be blunt, it's evident that you're no chemist. The fact of the matter is this: IUPAC is fine for small, simple things. But when you get onto the nasties like, for example, Unadecacyclo[9.9.0.01,5.02,12.02,18.03,7.06,10.08,12.011,15.013,17.016,20]eicosane, you'll understand why it is referred to using its common name, Pagodane. Or more frequently, with a diagram. Or less obscurely, Tricyclo[3.3.1.13,7]decane, a common substituent, and unanimously known as adamantane.
No I am not an exalted chemist like yourself. I am merely a biochemistry student. My comment is not as unheard of as you make it seem. I agree that the diagram makes things much easier for the viewer. I was discouraged because ChemSketch takes so much more effort than drawing by hand. Especially since I had not used chemsketch or uploaded anything before (copying every compound to paint and then saving and uploading and adding to the page...).
Your comment "Common nomenclature is outdated" is frankly wrong. It's certainly not unheard of, we hear it all the time from people who have just come into contact with chemistry.
A little learning is a dangerous thing, drink deep or taste not the pierian spring: there shallow draughts intoxicate the brain, and drinking largely sobers us again
Yes, drawing things by hand is a lot quicker, but it's not so helpful for getting stuff on wikipedia. My point is that you've got to use the right tool for the job. For common molecules, functional groups etc, then the common name is usually the way to go. For moderately complex things, IUPAC may be ok sometimes (2,3 dimethylsalicylic acid is easy enough), for anything more complicated, a diagram is probably necessary.
Given the vast number of chemical compounds I think it would be a good idea to create some kind of standard tutorial for how to create chemical diagrams and how to export them to wikipedia. Either that or have everyone just use IUPAC.
Also, I want to copy a visualization of a protein made with VMD here. Is there a standard program for visualizations, and how do copyrights work on them? Bensaccount22:30, 3 May 2004 (UTC)[reply]
Regarding a standard format, I agree. It would be helpful if we could come up with standard settings for the common software (chemdraw, isis, chemsketch) that would make things look smart.
I've been having thoughts about the balance between providing data and cluttering the page. A minimalist approach to the sidebar would be basic identification info (name, formula/structure, synonyms, CAS), and then external links to an MSDS and the NIST properties database. The next data to include would be the most useful basic properties (formula weight, phase transition temperatures, density). Some articles also feature some thermochemical data, and acid/base dissociation constants if applicable. One could also include stuff like index of refraction, dielectric constant, surface tension, etc...) but at some point, the properties sidebar gets to be longer than the text of the article, and the whole thing seems a bit silly.
There are a few pages I've made/heavily edited that link to organic table information that use tables inspired by the inorganic table information template. In making these, however, I came to realized that the appropriate information for any given compound varies rather heavily from compound to compound, and so the "definitive" organic table never came to pass. This is better shown by looking at a few of the pages and their tables, such as furfural, citric acid, and butadiene. Shimmin
I had created organic table information before I found this comment, but no regrets - it ought to exist if it's linked. I have raised it to a superset of the sold, liquid, gas, acid/base and hazardous type info. --Keith Edkins 21:54, 4 Jun 2004 (UTC)
I've made a template for the infobox. You can use {{subst:chembox}} to add it to articles. I merged the inorganic compound and organic compound tables into it; I think it covers everything one might be interested in. A few fields (such as the IUPAC name) might not be needed for inorganic compounds, but everything else should probably remain the same between the two. --Eequor 20:45, 15 Aug 2004 (UTC)
